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You might also want to verify that you have placed the JS calls and links in the correct locations. Some JS solutions need the call inside the HEAD section, some recommend directly after the opening body tag or directly before the closing body tag. This can be crucial if you also have popup links, expanded text, etc. in the same topic.
What I've done in RHx7 HTML is copy and paste the entire script into the Script dialogue box (Insert > HTML > Advanced > Script) and placing it directly under the Source tag. This works fine for me, even though it is not space-economical (having the script in every file rather than referencing it).
The script then appears in RH as a RED BOX. You may have to tweak the location of it to get it to work exactly as you want.
To save time (but not space), I just added the script to the templates where needed. Others more savvy than me can probably tell you a fool-proof way of calling out the scripts vice embedding them. I'm even using internal frameset scripts that point to external URL's (a poor man's RSS feed).